feat(merge): add pangraph merge command - #197

Merged

mmolari merged 54 commits into

Aug 19, 2026

Commits on Aug 10, 2026

docs(design): add design document for graph merge command
mmolari
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b55908f
fix(build): support building a graph from a single input sequence
mmolari
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57decee
Merge pull request #191 from neherlab/feat/merge-single-seq-build
mmolari
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bb7187a
feat(merge): add command to merge two pangenome graphs
mmolari
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59b48b1
feat(build): reject duplicate genome names, shared with merge
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82d126e
refactor(merge): drop unreachable relabeling retry loop
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2a599b1
refactor(pangraph): relabel graphs by value instead of in place
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5c9645f
refactor(pangraph): move sequence reconstruction into the graph module
mmolari
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25b7ca1
feat(pangraph): add name-keyed sequence verification
mmolari
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844db45
fix(build): verify reconstructed sequences by genome name, not by index
mmolari
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8627366
fix(reconstruct): match verification sequences by name
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db167ce
test: cover build --verify and name-keyed reconstruct verification
mmolari
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eea2d66

Commits on Aug 14, 2026

docs(tutorial): add page on merging two graphs
mmolari
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47e17de
docs: add changelog entries for the merge command
mmolari
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92e3b89
docs(design): mark merge roadmap as complete
mmolari
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dc44757
docs: add PR references to changelog
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5b40fdd
docs: remove merge design document
mmolari
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1f9e8de
test(merge): drop redundant sanity checks from the integration tests
mmolari
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755acf7
fix(merge): vary the relabeling salt so repeated merges do not collide
mmolari
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cb83e23
fix(cli): keep non-alignment options out of the Alignment help section
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2d77cce
refactor(merge): verify merged genomes one at a time
mmolari
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e6bb9e9
docs: simplify changelog
mmolari
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bad3c2b
Merge pull request #196 from neherlab/feat/merge-fixes
mmolari
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cc30583
fix(pangraph): reject unnamed and duplicate genome names in merge and simplify
mmolari
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4d51586
perf(reconstruct): drop redundant re-sort of an already-ordered path map
mmolari
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f03429c
refactor(reconstruct): drop redundant record reset before reading
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0c79a24
fix(reconstruct): elide long genome name lists in the verification error
mmolari
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daa927c
fix(cli): make the Default impl agree with the clap default for output paths
mmolari
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81f79c8
fix(pangraph): report malformed graph ids instead of panicking during relabel
mmolari
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166ab57
fix(cli): keep --jobs out of the Verbosity help section
mmolari
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c654879
test(cli): pin the help section of every argument
mmolari
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774a08c
docs: update changelog for merge and stricter genome id checks
mmolari
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e1f6dbc
fix(pangraph): reject empty genome and sequence names
mmolari
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8f5d2f8

Commits on Aug 17, 2026

Commits on Aug 18, 2026

Commits on Aug 19, 2026

docs: update changelog
mmolari
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84e6f9f